The first game of Boro's Slovenian tour saw Tony Mowbray use 18 different players and give a first senior outing to former Darlington striker Curtis Main.
Main was a second-half substitute, with Mowbray starting with Scott McDonald and Lee Miller up front, and a central midfield comprised of Cameron Park and Richie Smallwood.
Stephen McManus and Matthew Bates played alongside each other at the back, but an eighth-minute slip from the former allowed Tevfik Kose to fire Istanbul ahead.
The Turks almost doubled their lead before the break, but Danny Coyne, who could yet start the new season as Boro's first-choice goalkeeper in the absence of Jason Steele, tipped Mahmut Tekdemir's free-kick over the crossbar.
Boro's best chance came shortly after the hour mark, but Main failed to connect with the ball after good link-up play involving Leroy Lita and Adam Reach.
However, the Teessiders equalised in the 86th minute when Franks controlled the ball on his chest and looped a deft half-volley over the goalkeeper.
MIDDLESBROUGH (4-4-2): Coyne; McMahon, McManus (Grounds 60), Bates, Bennett; Hoyte (Franks 60), Smallwood (R Williams 70), Park (Bailey 70), Reach (Kink 70); McDonald (Lita 60), Miller (Main 70).